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Crystal structure of P. furiosus Mre11-H85S bound to a branched DNA and manganese
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1II7 PDB ENTRY 1II7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 40% PEG 200, 100 mM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.6 52.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.157 α = 90 b = 88.128 β = 90 c = 137.41 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 12.3.1 1.1159 ALS 12.3.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.2 50 98.5 0.071 20.1 6.1 47737 1 1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1II7 2.2 50 47737 45184 2402 98.52 0.20196 0.20196 0.19955 0.1985 0.24606 0.2464 RANDOM 43.32
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] -1.48 -1.68 3.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.374 r_dihedral_angle_4_deg 18.532 r_dihedral_angle_3_deg 15.92 r_dihedral_angle_1_deg 6.365 r_scangle_it 3.152 r_scbond_it 2.003 r_mcangle_it 1.553 r_angle_refined_deg 1.39 r_mcbond_it 0.933 r_nbtor_refined 0.315
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.374 r_dihedral_angle_4_deg 18.532 r_dihedral_angle_3_deg 15.92 r_dihedral_angle_1_deg 6.365 r_scangle_it 3.152 r_scbond_it 2.003 r_mcangle_it 1.553 r_angle_refined_deg 1.39 r_mcbond_it 0.933 r_nbtor_refined 0.315 r_symmetry_hbond_refined 0.271 r_symmetry_vdw_refined 0.199 r_xyhbond_nbd_refined 0.194 r_nbd_refined 0.18 r_chiral_restr 0.093 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5500 Nucleic Acid Atoms 473 Solvent Atoms 300 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing